LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTs
  3d grid and FFT values/proc = 103823 64000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50     4.311986    8083.3901    4729.9995    328.37487    3353.3906    1812.5186    685.40417    646.10358    50.083281    804.80656    1305984.8   -1306630.3    16960.287    48631.318    448.67988    116.22125 
     100     8.756623    6206.7865     3683.944    255.75365    2522.8425    977.52675    777.45439    838.58809    68.086914    471.97862    1306097.1   -1306707.9    15657.142    48631.318    380.53159    35.760643 
     150    13.134938    5386.0219     3582.482    248.70976    1803.5399    752.25928    803.04832    643.43249     49.76684    131.97853    1306139.2   -1306716.2    15140.102    48631.318    383.61303    10.880935 
     200    17.508189    4846.4097    3254.3932    225.93257    1592.0166    700.43329    812.26722    657.52279    51.044716   -64.045174    1306160.5   -1306725.7    13844.277    48631.318    351.90677    3.8489009 
     250    21.871676     4473.215    3091.5333     214.6262    1381.6817    688.24707    842.63267    590.45999     48.22798   -214.02425    1306156.6   -1306730.5    8808.7402    48631.318    335.32872    1.8372171 
     300    26.226064    4191.8834    2883.8468     200.2078    1308.0367    734.36657    856.15482    584.87904    47.590787   -343.44615    1306163.4   -1306734.9    3389.3777    48631.318    313.03581    1.3011826 
     350    30.568716    3972.0739    2756.8392    191.39044    1215.2347     664.4688    866.06348    580.13632    48.515297    -378.8729    1306173.3   -1306738.3    8458.1149    48631.318    299.31146    1.1345329 
     400    34.845648    3838.3528    2731.3975    189.62419    1106.9552     684.0318    870.67752    548.93014    44.038787    -460.1537    1306160.4     -1306741    6697.9188    48631.318    296.54405    1.1332149 
     450     39.17477      3731.18    2607.8585    181.04762    1123.3216    719.57572    894.99915    571.99504    47.625227   -537.60494    1306171.9   -1306745.2    2450.4224    48631.318    283.13713    1.0721818 
     500    43.497489    3607.0055    2565.9469    178.13796    1041.0586    717.36452    841.34375    551.39834    45.985413   -542.47313    1306170.9   -1306743.4    3077.1849    48631.318    278.59462    1.0410963 
     550    47.812038    3513.8132    2548.7259    176.94241    965.08736    673.81272    852.38161    522.99297    44.276434   -552.27379    1306171.2   -1306747.4    4659.7275    48631.318    276.70124    1.0757459 
     600    52.124423    3386.9627    2471.0692    171.55118    915.89348    689.99732    833.61298    517.49343    43.023588   -594.96363    1306170.6   -1306743.8    2159.7328    48631.318    268.27854    1.0287605 
     650    56.370068    3374.3191    2413.6719    167.56644    960.64717    703.32428    874.12028    535.41271    43.256032   -617.25815    1306168.6   -1306746.8    1262.4757    48631.318    261.99584    1.0950976 
     700    60.667476    3342.9467    2412.9563    167.51676    929.99042    683.70355    882.22521    527.03932    43.661355   -616.70117      1306161     -1306751    2950.9009    48631.318    261.92814    1.0771869 
     750    64.964696    3327.7938    2414.3547    167.61385    913.43902    695.12778    863.48248    542.99202    46.408369   -639.60076    1306160.7   -1306755.6    1583.0277    48631.318    262.09771    1.0464936 
     800    69.256916     3391.689    2452.2049    170.24155    939.48407     694.2176    892.61592    557.53726    45.495129   -654.56675    1306155.2     -1306751    1232.1671    48631.318    266.20601    1.0640309 
     850    73.527972    3386.8618    2486.6928    172.63584    900.16902     696.7684    880.27643    545.11446    46.474227   -665.90464    1306154.7   -1306757.3    1129.2062    48631.318    269.97945     1.027015 
     900    77.775993    3368.0724    2416.7145    167.77767    951.35789    718.66654    893.18396    537.79136    46.404626   -641.29596    1306152.9   -1306756.3    1673.0743    48631.318    262.34697    1.0597091 
     950    82.028341    3300.4793    2409.5613    167.28107      890.918    728.06888    890.51193    515.08456     44.36547   -671.13741    1306142.3   -1306758.2    1038.6579    48631.318    261.57036    1.0567234 
    1000    86.189789    3333.2955    2452.2486    170.24458    881.04692     699.8414    915.33862    506.83261     41.77374   -665.68264    1306141.6   -1306758.7    467.42142    48631.318    266.19104    1.0987814 
    1050    90.384168      3303.87    2376.9713    165.01854    926.89875    706.12941    930.65844    524.73304    42.644613   -657.19573    1306139.3   -1306759.4    1737.6624    48631.318    258.00246    1.0954432 
    1100    94.549452     3367.668    2454.9154    170.42973    912.75259    715.68494     935.8363    516.52205    43.261761   -671.86101    1306137.9   -1306764.6    961.79199    48631.318      266.492    1.0797548 
    1150     98.65493    3350.0898    2485.3993    172.54604    864.69051    699.23072    933.76405    510.60424    42.381362   -684.53513    1306127.1   -1306763.8   -272.48178    48631.318    269.82496    1.0512421 
    1200    102.82045    3309.6871    2398.9577    166.54492    910.72944    705.58979    934.53183    531.90967    45.872142   -664.58495    1306126.9   -1306769.5    627.31931    48631.318    260.41866    1.0531639 
    1250     106.9899     3304.504    2491.6998    172.98344    812.80426    710.83366    881.33764    494.90045     41.71618   -672.49264    1306123.8   -1306767.3    136.11723    48631.318    270.51026    1.0516137 
    1300    111.16224    3318.9543    2462.0621    170.92588    856.89219    709.17314    932.87209    503.80373    43.426006    -680.2474    1306121.2   -1306773.3    1276.2503    48631.318    267.28591    1.0510113 
    1350    115.27184    3314.8515    2434.8483    169.03659    880.00316    710.91641    922.28347    540.40795    44.753548   -686.09335    1306124.5   -1306776.7   -438.87694    48631.318    264.31236    1.0731666 
    1400    119.44228    3349.0785    2457.7697    170.62788    891.30875    711.28064    936.58607    516.63511    42.396287   -653.09763    1306113.8   -1306776.3    350.79618    48631.318    266.80555    1.0745043 
    1450    123.61267    3364.1486    2459.8741    170.77397    904.27455    696.57265    946.32098    538.55368     44.69075   -652.75091      1306111   -1306780.1    502.47466    48631.318    267.03201    1.0789056 
    1500    127.72962    3341.9369    2454.3302     170.3891    887.60672    726.46979    903.40815    557.73064    47.536125   -667.65025    1306100.7   -1306780.6    -248.0975    48631.318    266.44821     1.044725 
    1550    131.91041    3270.4282    2437.7916    169.24093    832.63655    691.49462    910.83807    523.17366     44.83093   -654.48655    1306100.5   -1306783.7    490.32965    48631.318    264.63652    1.0662604 
    1600     136.0834    3252.0725    2429.6805    168.67782    822.39196    689.68155    898.22828    535.31963     43.84399   -660.93277    1306100.1   -1306783.9    1729.5956    48631.318    263.74523    1.0817172 
    1650    140.26444     3239.748    2442.6258    169.57653    797.12222     671.1832     907.1659    507.03947    43.048028   -648.14001    1306103.3   -1306786.5    970.43988    48631.318    265.15987    1.0708872 
    1700     144.3855    3202.9157     2410.267    167.33006    792.64869    686.40974    882.40791    527.02899    43.819792   -656.82001      1306096   -1306786.2   -107.50166    48631.318    261.64368     1.062837 
    1750    148.56592    3214.6107    2366.3264    164.27953    848.28434    696.38228    915.58636     538.2236    47.852688    -652.7697    1306093.6   -1306790.6   -164.14366    48631.318    256.84519    1.0937744 
    1800    152.74611    3209.5771    2421.4089    168.10357    788.16819    683.61816    869.45802    532.77927    45.708374   -658.39221    1306103.1   -1306788.1    277.61781    48631.318    262.83282    1.1036154 
    1850    156.86567    3146.3973    2362.3333    164.00232      784.064    697.87032     875.8451    523.54452    43.851379   -665.83106    1306101.5   -1306792.7    497.88657    48631.318    256.42683    1.0654271 
    1900     161.0419    3141.5496    2367.1077    164.33378    774.44186    693.39945    878.97447    515.65653    44.619392   -668.11692    1306103.8   -1306793.9   -1427.3998    48631.318    256.94212    1.0727903 
    1950    165.22235    3134.6473     2295.577    159.36784    839.07025    699.62719    905.76937    519.32307    46.109334   -645.08933    1306104.9   -1306791.6    1744.2846    48631.318    249.19694    1.0064565 
    2000        169.4     3146.866    2361.3821    163.93628    785.48386    682.24124     889.6864    534.94877    46.855983    -678.1614      1306104   -1306794.1     699.8735    48631.318    256.32873    1.0559143 
Loop time of 169.4 on 1 procs for 2000 steps with 5500 atoms

Performance: 0.510 ns/day, 47.056 hours/ns, 11.806 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 107.93     | 107.93     | 107.93     |   0.0 | 63.71
Bond    | 19.76      | 19.76      | 19.76      |   0.0 | 11.66
Kspace  | 34.926     | 34.926     | 34.926     |   0.0 | 20.62
Neigh   | 1.9932     | 1.9932     | 1.9932     |   0.0 |  1.18
Comm    | 0.73555    | 0.73555    | 0.73555    |   0.0 |  0.43
Output  | 0.0065863  | 0.0065863  | 0.0065863  |   0.0 |  0.00
Modify  | 3.9135     | 3.9135     | 3.9135     |   0.0 |  2.31
Other   |            | 0.133      |            |       |  0.08

Nlocal:    5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    13219 ave 13219 max 13219 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.33739e+06 ave 1.33739e+06 max 1.33739e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1337388
Ave neighs/atom = 243.161
Ave special neighs/atom = 15.6364
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:02:49
